Notebook blog

Walking through the process of converting my pen-and-paper sketch of a decision tree into a computer graphic with graphviz.

Found a nifty tool for enforcing formatting styles for C code.

I tried out the Atom text editor very soon after it came out. For some reason--whether a half-hearted attempt on my part, or the fact that Atom was an unrefined beta--I didn't love it. After only a day or two, I reverted to the Komodo Edit editor I had been comfortable with for several years.

Recently, I heard a colleague …

I stumbled across the following question the other day in an email digest from Quora.

I have 5 years of working experience, but I still code very slow. How can I code faster? What should I learn?

Most of the responses don't answer the question directly, but instead make the point that speed is a very poor metric by which …

The UNIX shell is an indispensible tool for project organization and data management in bioinformatics. I spend a lot of time in the shell, and having picked up on a lot of time-saving techniques over the years it might just be my favorite computing environment.

The shell has its limitations, however. Piping, the very feature that gives the shell its …

Nifty trick for filtering stderr in the middle of a shell pipeline.

Today I was reformatting a manuscript and changing from a numbered citation style to an author/date citation style. In doing so, I found some issues with my EndNote references library that had gone unnoticed before since they were tucked away in the reference list. One of the issues involved citation of a paper with a single consortium author, designated …

My first research blog was a self-hosted Wordpress blog run from an Ubuntu server in our lab. I was initially enamored by the supposed control and flexibility this gave me, but when I changed institutions a year or so later I was not quite as enamored with the work that went into migrating the content, nor the time I spent …

Seed content for my new notebook.